Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,103,167 C→T 24.1% V196I (GTC→ATC)  agaR ← DNA‑binding transcriptional dual regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,103,1670CT24.1% 169.6 / 43.2 128V196I (GTC→ATC) agaRDNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base C (49/48);  new base T (19/12);  total (68/60)
Fisher's exact test for biased strand distribution p-value = 3.11e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.83e-01

Only 100 of 136 total aligned reads displayed.

TCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAATT  >  minE/2103118‑2103224
                                                 |                                                         
tCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAgatcgat                                         >  1:1600727/1‑68 (MQ=255)
tCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAgatcgat                                         >  1:1645134/1‑68 (MQ=255)
  atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:1933694/66‑1 (MQ=255)
  atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:177892/66‑1 (MQ=255)
  atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:1863140/66‑1 (MQ=255)
  atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:596629/66‑1 (MQ=255)
  atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:3011595/66‑1 (MQ=255)
  atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:2185042/66‑1 (MQ=255)
  atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:373298/66‑1 (MQ=255)
  atccaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:2241559/66‑1 (MQ=255)
   cacaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGatcgatcg                                       <  1:1150547/67‑1 (MQ=255)
   cacaTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGatcgatcg                                       <  1:1572798/67‑1 (MQ=255)
     caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:1573585/1‑47 (MQ=255)
     caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:2560158/1‑47 (MQ=255)
     caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:1026456/1‑47 (MQ=255)
     caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:1459503/1‑47 (MQ=255)
     caTCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:1384921/1‑47 (MQ=255)
     caTCCGA‑GGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGAcgc                                                         >  1:2406546/1‑46 (MQ=39)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCa                                                >  1:1072151/1‑52 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:2346141/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:2572461/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:695217/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:3377850/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:3089891/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:2078523/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:2460784/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:720468/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:3197591/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:1375257/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:1080344/1‑53 (MQ=37)
         cGACGGTTTAAACGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAg                                               >  1:891736/1‑53 (MQ=37)
         cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:23350/1‑68 (MQ=255)
         cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:1049361/1‑68 (MQ=255)
         cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:3206967/1‑68 (MQ=255)
         cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:1357226/1‑68 (MQ=255)
         cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:3334103/1‑68 (MQ=255)
         cGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTac                                >  1:137344/1‑68 (MQ=255)
             ggTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGc                                      <  1:1459222/58‑1 (MQ=255)
               tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:2682094/69‑1 (MQ=255)
               tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:3311860/69‑1 (MQ=255)
               tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:1052667/69‑1 (MQ=255)
               tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:3356325/69‑1 (MQ=255)
               tttAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGa                         <  1:3341766/69‑1 (MQ=255)
                 tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:324672/69‑1 (MQ=255)
                 tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:1007121/69‑1 (MQ=255)
                 tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:2310351/69‑1 (MQ=255)
                 tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:554498/69‑1 (MQ=255)
                 tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:842724/69‑1 (MQ=255)
                 tAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGaaa                       <  1:135974/69‑1 (MQ=255)
                    aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:1019265/68‑1 (MQ=255)
                    aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:1142688/68‑1 (MQ=255)
                    aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:595449/68‑1 (MQ=255)
                    aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:656072/68‑1 (MQ=255)
                    aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:3291636/68‑1 (MQ=255)
                    aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:1665351/68‑1 (MQ=255)
                    aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:709477/68‑1 (MQ=255)
                    aCGGGCTTCATCTTCATTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:1333328/68‑1 (MQ=255)
                     cGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAg                    <  1:2293073/68‑1 (MQ=255)
                     cGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAg                    <  1:2807827/68‑1 (MQ=255)
                     cGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGc                   <  1:842730/69‑1 (MQ=255)
                     cGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGc                   <  1:2205522/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:773543/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:672676/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:659086/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:3409095/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:574426/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:975683/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:1634288/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:2183564/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:2449542/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:3049416/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:2817396/69‑1 (MQ=255)
                      gAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  <  1:290084/69‑1 (MQ=255)
                         cttcatcttcatTATGCGTGCTGATGCCGCACTCCAGATCGATCGCATCTACACCAAGAAACa                     <  1:2913158/63‑1 (MQ=255)
                           tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:2797805/1‑64 (MQ=255)
                           tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:1082061/1‑64 (MQ=255)
                           tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:1550744/1‑64 (MQ=255)
                           tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:2403654/1‑64 (MQ=255)
                           tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:1736218/1‑64 (MQ=255)
                           tcatcttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCa                  >  1:464697/1‑64 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:1267048/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:100531/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:1676477/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:1784555/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:1840664/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2146767/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2261827/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:512596/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:459463/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:408744/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2514623/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATc                                   >  1:2675829/1‑42 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGt         >  1:448509/1‑68 (MQ=255)
                                ttcatTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGt         >  1:1147192/1‑68 (MQ=255)
                                      aTGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAAtt  >  1:1940604/1‑69 (MQ=255)
                                      aTGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAAtt  >  1:479114/1‑69 (MQ=255)
                                      aTGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAAtt  >  1:1278375/1‑69 (MQ=255)
                                      aTGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAAtt  >  1:2667601/1‑69 (MQ=255)
                                      aTGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAAtt  >  1:3297838/1‑69 (MQ=255)
                                               gACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAg                    <  1:2570533/42‑1 (MQ=255)
                                                 |                                                         
TCGCACATCCGACGGTTTAAACGAGCTTCATCTTCATTATGTGTGCTGACGCCGCGCTCCAGATCGATCGCATCTACACCAAGAAACAGCATATCGAAGTGGTAATT  >  minE/2103118‑2103224

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A